LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.8693370 3.8693370 3.8693370 Created orthogonal box = (0.0000000 -42.386463 0.0000000) to (8.6521006 42.386463 9.4779013) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1912603 5.6515284 6.3186009 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -42.386463 0.0000000) to (8.6521006 42.386463 9.4779013) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1912603 5.6515284 6.3186009 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -42.386463 0.0000000) to (8.6521006 42.386463 9.4779013) create_atoms CPU = 0.001 seconds 242 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 3 21 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_042691367780_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.526 | 4.526 | 4.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1127.3648 0 -1127.3648 112175.68 72 0 -1531.6207 0 -1531.6207 9231.5293 Loop time of 0.647579 on 1 procs for 72 steps with 480 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1127.3647861791 -1531.61959470453 -1531.62067314926 Force two-norm initial, final = 689.44878 0.10681006 Force max component initial, final = 175.31195 0.023638741 Final line search alpha, max atom move = 1.0000000 0.023638741 Iterations, force evaluations = 72 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63285 | 0.63285 | 0.63285 | 0.0 | 97.73 Neigh | 0.005617 | 0.005617 | 0.005617 | 0.0 | 0.87 Comm | 0.0050147 | 0.0050147 | 0.0050147 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0041 | | | 0.63 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3988.00 ave 3988 max 3988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75304.0 ave 75304 max 75304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75304 Ave neighs/atom = 156.88333 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.526 | 4.526 | 4.526 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -1531.6207 0 -1531.6207 9231.5293 6951.6983 77 0 -1531.7516 0 -1531.7516 -3.6878163 6995.2405 Loop time of 0.0433801 on 1 procs for 5 steps with 480 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1531.62067314926 -1531.75156390921 -1531.75158345702 Force two-norm initial, final = 69.758064 0.15461904 Force max component initial, final = 44.639242 0.051142536 Final line search alpha, max atom move = 0.0043525004 0.00022259791 Iterations, force evaluations = 5 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041699 | 0.041699 | 0.041699 | 0.0 | 96.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029862 | 0.00029862 | 0.00029862 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001383 | | | 3.19 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3958.00 ave 3958 max 3958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74448.0 ave 74448 max 74448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74448 Ave neighs/atom = 155.10000 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1531.7516 0 -1531.7516 -3.6878163 Loop time of 2.228e-06 on 1 procs for 0 steps with 480 atoms 179.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.228e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3928.00 ave 3928 max 3928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70972.0 ave 70972 max 70972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70972 Ave neighs/atom = 147.85833 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1531.7516 -1531.7516 8.6715947 85.050475 9.4847729 -3.6878163 -3.6878163 7.9384686 -11.751939 -7.2499784 2.5215654 323.88508 Loop time of 2.138e-06 on 1 procs for 0 steps with 480 atoms 187.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.138e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3928.00 ave 3928 max 3928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35486.0 ave 35486 max 35486 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70972.0 ave 70972 max 70972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70972 Ave neighs/atom = 147.85833 Neighbor list builds = 0 Dangerous builds = 0 480 -1531.75158345702 eV 2.52156539914621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01